Comparative studies addressing the variation in how complex adaptive traits can be genetically regulated provide basic insights into the diverse diagnosis and treatments that may be needed to effectively target disease. Heliconius butterfly species H. erato and H. melpomene exhibit parallel color pattern diversifications across the Neotropics, forming up to 30 mimicry complexes. This highly tractable system provides numerous examples of color pattern convergence and divergence, and thus serves as a proxy for understanding the genetic regulation of rapidly evolving complex phenotypes. The genetic switches responsible for the diverse color patterns in these species have been narrowed to three loci, two of which have been refined to a genomic interval of ~400KB each. The proposed study seeks to hone in on the genes responsible for both divergent and convergent color pattern phenotypes in these butterflies. Towards this goal, microarrays containing both DNA tiled across these loci and whole-genomic transcripts will be hybridized to wing tissues across six developmental stages from five color pattern races of H. erato. Analyses of differential hybridization on these arrays will be used to assess the genes responsible for color pattern differences within each locus, the gene modules and hypothetical pathways elicited by these regulatory genes, and the genetic interactions between these pathways. Rapidly evolving traits may have high variance or even non-functionality in their underlying gene expression. Tissues of multiple individuals of each color pattern race will be hybridized to microarrays to explore the natural variation in gene expression across candidate genes. Genes implicated in color pattern will be analyzed further using spatial analysis of RNA and protein expression in wing tissue using in situ hybridization and antibodies. Public Health Relevance: By examining the genetics behind diverse mimetic color patterns of butterflies we gain a model system for understanding how genetic interactions and gene architecture govern changes in complex traits with a high impact on survival. This will enhance understanding of the genetic regulation of the complex adaptive traits of disease and disease resistance and, therefore, highlight the multitude of strategies that may be needed to both diagnose and treat disease.